Mercurial > repos > rmarenco > hubarchivecreator

comparison hubArchiveCreator.xml @ 22:7ddf651457df draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
author yating-l
date Wed, 12 Apr 2017 17:03:51 -0400
parents 884ee2a71680
children 2677f1899aa8
comparison
equal deleted inserted replaced
21:884ee2a71680 22:7ddf651457df
102 #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option" 102 #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option"
103 --bedBlastAlignments $f.formatChoice.bedChoice.BED_blast_alignment 103 --bedBlastAlignments $f.formatChoice.bedChoice.BED_blast_alignment
104 #silent $prepare_json($f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final, 104 #silent $prepare_json($f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final,
105 extra_data_dict) 105 extra_data_dict)
106 #end if 106 #end if
107 #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option"
108 --bigpsl $f.formatChoice.bedChoice.BED_blat_alignment
109 #silent $prepare_json($f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final,
110 extra_data_dict)
111 #end if
107 #end if 112 #end if
108 #if $f.formatChoice.format_select == "psl" 113 #if $f.formatChoice.format_select == "psl"
109 --psl $f.formatChoice.PSL 114 --psl $f.formatChoice.PSL
110 #silent $prepare_json($f.formatChoice.PSL, $index_track_final, 115 #silent $prepare_json($f.formatChoice.PSL, $index_track_final,
111 extra_data_dict) 116 extra_data_dict)
123 #if $f.formatChoice.format_select == "gtf" 128 #if $f.formatChoice.format_select == "gtf"
124 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8 129 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8
125 --gtf $f.formatChoice.GTF 130 --gtf $f.formatChoice.GTF
126 #silent $prepare_json($f.formatChoice.GTF, $index_track_final, 131 #silent $prepare_json($f.formatChoice.GTF, $index_track_final,
127 extra_data_dict) 132 extra_data_dict)
128 #end if
129 #if $f.formatChoice.format_select == "bigpsl"
130 --bigpsl $f.formatChoice.BIGPSL
131 #silent $prepare_json($f.formatChoice.BIGPSL, $index_track_final,
132 extra_data_dict)
133 #end if 133 #end if
134 #end for 134 #end for
135 #end for 135 #end for
136 136
137 ## We combine the fasta file dataset name with his false path in a JSON object 137 ## We combine the fasta file dataset name with his false path in a JSON object
179 <option value="bed">BED</option> 179 <option value="bed">BED</option>
180 <option value="psl">PSL</option> 180 <option value="psl">PSL</option>
181 <option value="bigwig">BIGWIG</option> 181 <option value="bigwig">BIGWIG</option>
182 <option value="gff3">GFF3</option> 182 <option value="gff3">GFF3</option>
183 <option value="gtf">GTF</option> 183 <option value="gtf">GTF</option>
184 <option value="bigpsl">BigPsl</option>
185 </param> 184 </param>
186 185
187 <when value="bam"> 186 <when value="bam">
188 <param 187 <param
189 format="bam" 188 format="bam"
204 <conditional name="bedChoice"> 203 <conditional name="bedChoice">
205 <param name="bed_select" type="select" label="Bed Choice"> 204 <param name="bed_select" type="select" label="Bed Choice">
206 <option value="bed_generic" selected="true">BED Generic (bed3+)</option> 205 <option value="bed_generic" selected="true">BED Generic (bed3+)</option>
207 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option> 206 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
208 <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option> 207 <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option>
209 <option value="bed_blast_alignment_option">BED Blast alignments (bed12+12 / bigPsl.as)</option> 208 <option value="bed_blast_alignment_option">Blast alignments (bed12+12 / bigPsl.as)</option>
209 <option value="bed_blat_alignment_option">BLAT alignments (bigPsl / bigPsl.as)</option>
210 </param> 210 </param>
211 <when value="bed_generic"> 211 <when value="bed_generic">
212 <param 212 <param
213 format="bed" 213 format="bed"
214 name="BED" 214 name="BED"
237 <param 237 <param
238 format="bed" 238 format="bed"
239 name="BED_blast_alignment" 239 name="BED_blast_alignment"
240 type="data" 240 type="data"
241 label="Bed Blast Alignments (Bed12+12) File" 241 label="Bed Blast Alignments (Bed12+12) File"
242 />
243 </when>
244 <when value="bed_blat_alignment_option">
245 <param
246 format="bed"
247 name="BED_blat_alignment"
248 type="data"
249 label="Bed BLAT Alignments (bigPsl) File"
242 /> 250 />
243 </when> 251 </when>
244 </conditional> 252 </conditional>
245 <param name="track_color" type="color" label="Track color" value="#000000"> 253 <param name="track_color" type="color" label="Track color" value="#000000">
246 <sanitizer> 254 <sanitizer>
308 <add value="#"/> 316 <add value="#"/>
309 </valid> 317 </valid>
310 </sanitizer> 318 </sanitizer>
311 </param> 319 </param>
312 </when> 320 </when>
313 <when value="bigpsl">
314 <param
315 format="bigpsl"
316 name="BIGPSL"
317 type="data"
318 label="bigPsl File"
319 />
320 <param name="track_color" type="color" label="Track color" value="#000000">
321 <sanitizer>
322 <valid initial="string.letters,string.digits">
323 <add value="#"/>
324 </valid>
325 </sanitizer>
326 </param>
327 </when>
328 </conditional> 321 </conditional>
329 </repeat> 322 </repeat>
330 </repeat> 323 </repeat>
331 <conditional name="advanced_options"> 324 <conditional name="advanced_options">
332 <param name="advanced_options_selector" type="select" label="Advanced options"> 325 <param name="advanced_options_selector" type="select" label="Advanced options">